Topic
Fantom
About: Fantom is a research topic. Over the lifetime, 42 publications have been published within this topic receiving 1036 citations.
Papers
TL;DR: The recent updates of both data and interfaces in the FANTOM web resource are reported, including expansion of the resource by employing different assays, which yielded additional atlases of long noncoding RNAs, miRNAs and their promoters.
Abstract: The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.
259 citations
TL;DR: The international Functional Annotation Of the Mammalian Genomes 4 research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments.
Abstract: In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and under 52 systematic siRNA perturbations. In addition, data regarding chromatin status derived from ChIP-chip to elucidate the transcriptional regulatory interactions are included. Here we present these data to the research community as an integrated web resource.
79 citations
TL;DR: EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns.
Abstract: EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and search patterns. The FANTOM4 EdgeExpress database http://fantom.gsc.riken.jp/4/ edgeexpress summarizes gene expression patterns in the context of alternative promoter structures and regulatory transcription factors and microRNAs using intuitive gene-centric and sub-network views. This is an important resource for gene regulation in acute myeloid leukemia, monocyte/macrophage differentiation and human transcriptional networks.
76 citations
18 Nov 2010
TL;DR: This thesis investigates how a popular new way of distributed computing called service orientation can be used within the field of Knowledge Discovery, and applies this model to create a web service, Fantom, that mines subgroups in a ranked list of identifiers, based on their score.
Abstract: In this thesis we will investigate how a popular new way of distributed computing called service orientation can be used within the field of Knowledge Discovery. We critically investigate its principles and present models for developing withing this paradigm. We then apply this model to create a web service caled Fantom, that mines subgroups in a ranked list of identifiers, based on their score. The descriptions of these subgroups are done in ontologies to provide the scientist a description in a standardized and familiar language. Finally, Fantom is tested on two different data sets from the field of life-sciences; one concerning gene data, the other concerning SNP data.
66 citations
TL;DR: FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of Riken full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms.
Abstract: FANTOM DB, the database of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to store sequence information of RIKEN full-length enriched mouse cDNA clones, graphical views of sequence analysis results, curated functional annotation information and additional descriptions, including Gene Ontology terms. RIKEN’s Mouse Gene Encyclopedia Project aims to collect full-length enriched cDNA clones from various mouse tissues, determine the full-length nucleotide sequences, infer their chromosomal locations by computer and characterize gene expression patterns. FANTOM DB has been developed to facilitate this work and to facilitate functional genomic studies such as positional candidate cloning, cDNA microarrays and protein interaction analyses. FANTOM DB contains 21 076 full-length cDNA sequences with rich functional annotations and is publicly available. FANTOM DB thus provides curated functional annotation to RIKEN full-length enriched mouse clones, and has links to other public resources. FANTOM DB can be accessed at http://fantom.gsc.riken.go.jp/db/.
62 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2021 | 1 |
| 2020 | 2 |
| 2019 | 4 |
| 2018 | 2 |
| 2017 | 3 |
| 2016 | 2 |